FHIR Osiris Implementation Guide
2.1.0 - ci-build

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Resource Profile: Variant Copy Number

Official URL: https://build.fhir.org/ig/arkhn/arkhn-ig-osiris/StructureDefinition/copy-number Version: 2.1.0
Active as of 2023-04-10 Computable Name: CopyNumber

Observation of a Copy Number variant derived from a SequencingAnalysis. The CopyNumber profile is used to indicate the pathogenicity, the actionability, the loss of heterozygosity, the cytogenetic location, the start - end positions, the reference sequence assembly, the variation code, the segment intensity, the number of copy found and the Copy Number segment size.

Usage:

  • Refer to this Resource Profile:

Formal Views of Profile Content

Description of Profiles, Differentials, Snapshots and how the different presentations work.

This structure is derived from Variant

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation 0..*VariantVariant
... subject 0..1Reference(Oncology Patient)Who and/or what the observation is about
... Slices for derivedFrom 1..*Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence)Related measurements the observation is made from
Slice: Unordered, Open by pattern:reference
.... derivedFrom:Analysis 1..1Reference(Sequencing Analysis)Analysis from which come this observation
.... component:cytogenetic-location 0..*BackboneElementCytogenetic (chromosome) location
.... component:ref-sequence-assembly 0..*BackboneElementHuman reference sequence assembly version
..... valueCodeableConcept 1..1CodeableConceptActual component result
.... component:variation-code 0..1BackboneElementVariation Code
..... valueCodeableConcept 1..1CodeableConceptActual component result
.... component:copy-number 0..1BackboneElementGenomic structural variant copy number
..... valueQuantity 1..1CountA measured or measurable amount
.... component:exact-start-end 0..1BackboneElementExact start-end
..... valueRange 1..1RangeActual component result
...... low 1..1SimpleQuantityExact Start
...... high 0..1SimpleQuantityExact End
.... component:variant-length 0..1BackboneElementStructural variant length
.... component:actionability 0..1BackboneElementConclusion of the clinicians wether the variant is actionable or not during the Molecular Tumor Board
..... code 1..1CodeableConceptType of component observation (code / type)
Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 93348-1
..... value[x] 0..1booleanActual component result
Slice: Unordered, Open by type:$this
..... valueBoolean 0..1booleanActual component result
.... component:proposed-for-orientation 0..1BackboneElementIs the ClinicalTumorBoardConclusion used to orient the treatment decision ?
..... code 1..1CodeableConceptType of component observation (code / type)
Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/umls
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: C0449889
..... value[x] 0..1booleanActual component result
Slice: Unordered, Open by type:$this
..... valueBoolean 0..1booleanActual component result
.... component:pathogenicity 0..1BackboneElementConclusion of the biologist on the pathogenicity of the variant before the Molecular Tumor Board
..... code 1..1CodeableConceptType of component observation (code / type)
Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 74019-1
..... value[x] 0..1CodeableConceptActual component result
Slice: Unordered, Open by type:$this
Binding: Pathogenicity Value Set (required)
..... valueCodeableConcept 0..1CodeableConceptActual component result
.... component:loss-of-heterozygosity 0..1BackboneElementIs the segment located in a region of loss of heterozygosity ? (can be independant from copy number information
..... code 1..1CodeableConceptType of component observation (code / type)
Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/umls
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: C1881449
..... value[x] 0..1booleanActual component result
Slice: Unordered, Open by type:$this
..... valueBoolean 0..1booleanActual component result
.... component:segment-intensity 0..1BackboneElementIntensity of the measured signal
..... code 1..1CodeableConceptType of component observation (code / type)
Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/umls
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: C2732930
..... value[x] 0..1integerActual component result
Slice: Unordered, Open by type:$this
..... valueInteger 0..1integerActual component result

doco Documentation for this format

Terminology Bindings (Differential)

PathConformanceValueSet
Observation.component:pathogenicity.value[x]requiredPathogenicity
NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation C0..*VariantVariant
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... BodyStructure 0..1Reference(BodyStructure)Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
... SecondaryFinding 0..1CodeableConceptSecondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings
URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding
Binding: ObservationCategoryCodes (extensible): Codes to denote a guideline or policy statement.when a genetic test result is being shared as a secondary finding.


... status ?!Σ1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.

... category 1..*CodeableConceptClassification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.



Required Pattern: At least the following
.... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
..... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
... code Σ1..1CodeableConceptGenetic variant assessment
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
.... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
..... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: 69548-6
... subject Σ0..1Reference(Oncology Patient)Who and/or what the observation is about
... Slices for effective[x] Σ0..1dateTimeClinically relevant time/time-period for observation
Slice: Unordered, Closed by type:$this
.... effective[x]:effectiveDateTime Σ0..1dateTimeClinically relevant time/time-period for observation
... performer Σ0..1Reference(Practitioner | Organization | Patient | RelatedPerson)Who is responsible for the observation
... value[x] ΣC1..1CodeableConceptPresent|Absent|No call|Indeterminate
Binding: LOINC Answer List LL1971-2 (required): Genetic Variant Assessment

... Slices for derivedFrom Σ1..*Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence)Related measurements the observation is made from
Slice: Unordered, Open by pattern:reference
.... derivedFrom:Analysis Σ1..1Reference(Sequencing Analysis)Analysis from which come this observation
... Slices for component Σ0..*BackboneElementComponent results
Slice: Unordered, Open by pattern:code
.... component:All Slices Content/Rules for all slices
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.

.... component:gene-studied Σ0..*BackboneElementGene studied ID
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48018-6
..... value[x] Σ1..1CodeableConceptIf no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HGNC (extensible): HGNC: Human Gene Nomenclature Committee

.... component:cytogenetic-location Σ0..*BackboneElementCytogenetic (chromosome) location
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48001-2
..... value[x] Σ1..1CodeableConceptActual component result
Binding: (unbound) (example): Binding not yet defined

.... component:ref-sequence-assembly Σ0..*BackboneElementHuman reference sequence assembly version
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 62374-4
..... value[x] Σ1..1CodeableConceptActual component result
Binding: LOINC Answer List LL1040-6 (extensible): Human reference sequence NCBI build IDs

.... component:dna-chg Σ0..1BackboneElementDNA Change - Transcript (cHGVS)
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48004-6
..... value[x] Σ1..1CodeableConceptActual component result
Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society

.... component:dna-chg-type Σ0..1BackboneElementDNA change type
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48019-4
..... value[x] Σ1..1CodeableConceptConcepts in sequence ontology under SO:0002072 (see http://www.sequenceontology.org/browser/current_release/term/SO:0002072)
Binding: DNA Change Type (extensible): DNA Change type values (Sequence Ontology)

.... component:functional-annotation Σ0..*BackboneElementFunctional Annotation
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: functional-annotation
..... value[x] Σ1..1CodeableConceptConcepts in sequence ontology under SO:0001537 (see http://www.sequenceontology.org/browser/current_release/term/SO:0001537)
Binding: Functional Annotation (extensible): Functional Annotation (Sequence Ontology)

.... component:variation-code Σ0..1BackboneElementVariation Code
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81252-9
..... value[x] Σ1..1CodeableConceptActual component result
Binding: (unbound) (example): Binding not yet defined

.... component:dbSNP-id Σ0..1BackboneElementdbSNP ID
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81255-2
..... value[x] Σ1..1CodeableConceptActual component result
Binding: (unbound) (example): Binding not yet defined

.... component:genomic-dna-chg Σ0..1BackboneElementDNA Change - Genomic (gHGVS)
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81290-9
..... value[x] Σ1..1CodeableConceptActual component result
Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society

.... component:genomic-source-class Σ0..1BackboneElementGenomic source class
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48002-0
..... value[x] Σ1..1CodeableConceptGermline | Somatic | Fetal | Likely germline | Likely somatic |Likely fetal | Unknown genomic origin | De novo
Binding: LOINC Answer List LL378-1 (extensible): Genomic source class values

.... component:amino-acid-chg Σ0..1BackboneElementAmino acid change (pHGVS)
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48005-3
..... value[x] Σ1..1CodeableConceptActual component result
Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society

.... component:amino-acid-chg-type Σ0..1BackboneElementAmino acid change type
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48006-1
..... value[x] Σ1..1CodeableConceptWild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Silent | Stop Codon Mutation
Binding: LOINC Answer List LL380-7 (required): Amino acid change type values

.... component:transcript-ref-seq Σ0..1BackboneElementTranscript reference sequence ID
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 51958-7
..... value[x] Σ1..1CodeableConceptActual component result
Binding: (unbound) (example): Binding not yet defined

.... component:genomic-ref-seq Σ0..1BackboneElementGenomic reference sequence ID
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48013-7
..... value[x] Σ1..1CodeableConceptActual component result
Binding: (unbound) (example): Binding not yet defined

.... component:sample-allelic-frequency Σ0..1BackboneElementSample Allelic Frequency
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptSample Sample VAF
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81258-6
..... value[x] Σ1..1QuantityActual component result
...... value Σ1..1decimalNumerical value (with implicit precision)
...... comparator ?!Σ0..1code< | <= | >= | > - how to understand the value
Binding: QuantityComparator (required): How the Quantity should be understood and represented.

...... system ΣC1..1uriSystem that defines coded unit form
Fixed Value: http://unitsofmeasure.org
.... component:allelic-read-depth Σ0..*BackboneElementAllelic read depth
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 82121-5
..... value[x] Σ1..1QuantityActual component result
.... component:allelic-state Σ0..1BackboneElementAllelic state
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 53034-5
..... value[x] Σ1..1CodeableConceptHeteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (extensible): Allelic state type values

.... component:copy-number Σ0..1BackboneElementGenomic structural variant copy number
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 82155-3
..... value[x] C1..1CountA measured or measurable amount
.... component:ref-allele Σ0..1BackboneElementGenomic ref allele
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 69547-8
..... value[x] Σ1..1stringActual component result
.... component:alt-allele Σ0..1BackboneElementGenomic alt allele
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 69551-0
..... value[x] Σ1..1stringActual component result
.... component:coordinate-system Σ0..1BackboneElementCoordinate System
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 92822-6
..... value[x] Σ1..1CodeableConcept0-based interval | 0-based character | 1-based character
Binding: LOINC Answer List LL5323-2 (preferred): Base coordinate systems start and end measurements for variants

.... component:exact-start-end Σ0..1BackboneElementExact start-end
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: exact-start-end
..... value[x] Σ1..1RangeActual component result
...... low Σ1..1SimpleQuantityExact Start
.... component:variant-length Σ0..1BackboneElementStructural variant length
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81300-6
..... value[x] C1..1CountA measured or measurable amount
.... component:outer-start-end Σ0..1BackboneElementVariant outer start and end
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: outer-start-end
..... value[x] Σ1..1RangeActual component result
...... low Σ1..1SimpleQuantityLow limit
...... high Σ1..1SimpleQuantityHigh limit
.... component:inner-start-end Σ0..1BackboneElementVariant inner start and end
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: inner-start-end
..... value[x] Σ1..1RangeActual component result
...... low Σ1..1SimpleQuantityLow limit
...... high Σ1..1SimpleQuantityHigh limit
.... component:chromosome-copy-number-change-type Σ0..1BackboneElementChromosome copy number change type
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 62378-5
..... value[x] Σ1..1CodeableConceptCopy number gain | Copy number loss
Binding: LOINC Answer List LL1041-4 (required): Copy Number Change Types

.... component:arrCGH-ratio Σ0..1BackboneElementStructural variant reported arrCGH [Ratio]
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81299-0
..... value[x] C1..1SimpleQuantityA fixed quantity (no comparator)
.... component:complex-var-type Σ0..1BackboneElementComplex variant type
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81263-6
..... value[x] Σ1..1CodeableConceptCompound heterozygous | Double heterozygous | Haplotype | Hemizygous
Binding: LOINC Answer List LL3999-1 (required): Complex variant type

.... component:cytogenomic-nomenclature Σ0..1BackboneElementCytogenomic Nomenclature
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptVariant ISCN
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81291-7
..... value[x] Σ1..1CodeableConceptActual component result
Binding: (unbound) (example): Binding not yet defined

.... component:variant-inheritance Σ0..1BackboneElementVariant Inheritance
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: variant-inheritance
..... value[x] Σ1..1CodeableConceptActual component result
Binding: Variant Inheritance (extensible): Variant Inheritance (Sequence Ontology)

.... component:actionability Σ0..1BackboneElementConclusion of the clinicians wether the variant is actionable or not during the Molecular Tumor Board
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 93348-1
..... Slices for value[x] Σ0..1booleanActual component result
Slice: Unordered, Closed by type:$this
...... value[x]:valueBoolean Σ0..1booleanActual component result
.... component:proposed-for-orientation Σ0..1BackboneElementIs the ClinicalTumorBoardConclusion used to orient the treatment decision ?
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/umls
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: C0449889
..... Slices for value[x] Σ0..1booleanActual component result
Slice: Unordered, Closed by type:$this
...... value[x]:valueBoolean Σ0..1booleanActual component result
.... component:pathogenicity Σ0..1BackboneElementConclusion of the biologist on the pathogenicity of the variant before the Molecular Tumor Board
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 74019-1
..... Slices for value[x] Σ0..1CodeableConceptActual component result
Slice: Unordered, Closed by type:$this
Binding: Pathogenicity Value Set (required)
...... value[x]:valueCodeableConcept Σ0..1CodeableConceptActual component result
.... component:loss-of-heterozygosity Σ0..1BackboneElementIs the segment located in a region of loss of heterozygosity ? (can be independant from copy number information
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/umls
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: C1881449
..... Slices for value[x] Σ0..1booleanActual component result
Slice: Unordered, Closed by type:$this
...... value[x]:valueBoolean Σ0..1booleanActual component result
.... component:segment-intensity Σ0..1BackboneElementIntensity of the measured signal
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/umls
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: C2732930
..... Slices for value[x] Σ0..1integerActual component result
Slice: Unordered, Closed by type:$this
...... value[x]:valueInteger Σ0..1integerActual component result

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet / Code
Observation.statusrequiredObservationStatus
Observation.categorypreferredPattern: laboratory
Observation.codeexamplePattern: LOINC code 69548-6
Observation.value[x]requiredLOINC LL1971-2
Observation.component.codeexampleLOINCCodes (a valid code from LOINC)
Observation.component:gene-studied.codeexamplePattern: LOINC code 48018-6
Observation.component:gene-studied.value[x]extensibleHGNC
Observation.component:cytogenetic-location.codeexamplePattern: LOINC code 48001-2
Observation.component:cytogenetic-location.value[x]example
Observation.component:ref-sequence-assembly.codeexamplePattern: LOINC code 62374-4
Observation.component:ref-sequence-assembly.value[x]extensibleLOINC LL1040-6
Observation.component:dna-chg.codeexamplePattern: LOINC code 48004-6
Observation.component:dna-chg.value[x]requiredHGVS
Observation.component:dna-chg-type.codeexamplePattern: LOINC code 48019-4
Observation.component:dna-chg-type.value[x]extensibleDnaChangeType
Observation.component:functional-annotation.codeexamplePattern: functional-annotation
Observation.component:functional-annotation.value[x]extensibleFunctionalAnnotation
Observation.component:variation-code.codeexamplePattern: LOINC code 81252-9
Observation.component:variation-code.value[x]example
Observation.component:dbSNP-id.codeexamplePattern: LOINC code 81255-2
Observation.component:dbSNP-id.value[x]example
Observation.component:genomic-dna-chg.codeexamplePattern: LOINC code 81290-9
Observation.component:genomic-dna-chg.value[x]requiredHGVS
Observation.component:genomic-source-class.codeexamplePattern: LOINC code 48002-0
Observation.component:genomic-source-class.value[x]extensibleLOINC LL378-1
Observation.component:amino-acid-chg.codeexamplePattern: LOINC code 48005-3
Observation.component:amino-acid-chg.value[x]requiredHGVS
Observation.component:amino-acid-chg-type.codeexamplePattern: LOINC code 48006-1
Observation.component:amino-acid-chg-type.value[x]requiredLOINC LL380-7
Observation.component:transcript-ref-seq.codeexamplePattern: LOINC code 51958-7
Observation.component:transcript-ref-seq.value[x]example
Observation.component:genomic-ref-seq.codeexamplePattern: LOINC code 48013-7
Observation.component:genomic-ref-seq.value[x]example
Observation.component:sample-allelic-frequency.codeexamplePattern: LOINC code 81258-6
Observation.component:sample-allelic-frequency.value[x].comparatorrequiredQuantityComparator
Observation.component:allelic-read-depth.codeexamplePattern: LOINC code 82121-5
Observation.component:allelic-state.codeexamplePattern: LOINC code 53034-5
Observation.component:allelic-state.value[x]extensibleLOINC LL381-5
Observation.component:copy-number.codeexamplePattern: LOINC code 82155-3
Observation.component:ref-allele.codeexamplePattern: LOINC code 69547-8
Observation.component:alt-allele.codeexamplePattern: LOINC code 69551-0
Observation.component:coordinate-system.codeexamplePattern: LOINC code 92822-6
Observation.component:coordinate-system.value[x]preferredLOINC LL5323-2
Observation.component:exact-start-end.codeexamplePattern: exact-start-end
Observation.component:variant-length.codeexamplePattern: LOINC code 81300-6
Observation.component:outer-start-end.codeexamplePattern: outer-start-end
Observation.component:inner-start-end.codeexamplePattern: inner-start-end
Observation.component:chromosome-copy-number-change-type.codeexamplePattern: LOINC code 62378-5
Observation.component:chromosome-copy-number-change-type.value[x]requiredLOINC LL1041-4
Observation.component:arrCGH-ratio.codeexamplePattern: LOINC code 81299-0
Observation.component:complex-var-type.codeexamplePattern: LOINC code 81263-6
Observation.component:complex-var-type.value[x]requiredLOINC LL3999-1
Observation.component:cytogenomic-nomenclature.codeexamplePattern: LOINC code 81291-7
Observation.component:cytogenomic-nomenclature.value[x]example
Observation.component:variant-inheritance.codeexamplePattern: variant-inheritance
Observation.component:variant-inheritance.value[x]extensibleVariantInheritance
Observation.component:actionability.codeexamplePattern: LOINC code 93348-1
Observation.component:proposed-for-orientation.codeexamplePattern: C0449889
Observation.component:pathogenicity.codeexamplePattern: LOINC code 74019-1
Observation.component:pathogenicity.value[x]requiredPathogenicity
Observation.component:loss-of-heterozygosity.codeexamplePattern: C1881449
Observation.component:segment-intensity.codeexamplePattern: C2732930
NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation C0..*VariantVariant
... id Σ0..1idLogical id of this artifact
... meta Σ0..1MetaMetadata about the resource
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: CommonLanguages (preferred): A human language.

Additional BindingsPurpose
AllLanguagesMax Binding
... text 0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... Slices for extension 0..*ExtensionExtension
Slice: Unordered, Open by value:url
... BodyStructure 0..1Reference(BodyStructure)Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
... SecondaryFinding 0..1CodeableConceptSecondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings
URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding
Binding: ObservationCategoryCodes (extensible): Codes to denote a guideline or policy statement.when a genetic test result is being shared as a secondary finding.


... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier Σ0..*IdentifierBusiness Identifier for observation
... basedOn Σ0..*Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)Fulfills plan, proposal or order
... partOf Σ0..*Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy)Part of referenced event
... status ?!Σ1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.

... category 1..*CodeableConceptClassification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.



Required Pattern: At least the following
.... id0..1idUnique id for inter-element referencing
.... extension0..*ExtensionAdditional content defined by implementations
.... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
..... id0..1idUnique id for inter-element referencing
..... extension0..*ExtensionAdditional content defined by implementations
..... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
..... version0..1stringVersion of the system - if relevant
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
..... display0..1stringRepresentation defined by the system
..... userSelected0..1booleanIf this coding was chosen directly by the user
.... text0..1stringPlain text representation of the concept
... code Σ1..1CodeableConceptGenetic variant assessment
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
.... id0..1idUnique id for inter-element referencing
.... extension0..*ExtensionAdditional content defined by implementations
.... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
..... id0..1idUnique id for inter-element referencing
..... extension0..*ExtensionAdditional content defined by implementations
..... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
..... version0..1stringVersion of the system - if relevant
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: 69548-6
..... display0..1stringRepresentation defined by the system
..... userSelected0..1booleanIf this coding was chosen directly by the user
.... text0..1stringPlain text representation of the concept
... subject Σ0..1Reference(Oncology Patient)Who and/or what the observation is about
... focus ΣTU0..*Reference(Resource)What the observation is about, when it is not about the subject of record
... encounter Σ0..1Reference(Encounter)Healthcare event during which this observation is made
... Slices for effective[x] Σ0..1dateTimeClinically relevant time/time-period for observation
Slice: Unordered, Closed by type:$this
.... effective[x]:effectiveDateTime Σ0..1dateTimeClinically relevant time/time-period for observation
... issued Σ0..1instantDate/Time this version was made available
... performer Σ0..1Reference(Practitioner | Organization | Patient | RelatedPerson)Who is responsible for the observation
... value[x] ΣC1..1CodeableConceptPresent|Absent|No call|Indeterminate
Binding: LOINC Answer List LL1971-2 (required): Genetic Variant Assessment

... dataAbsentReason C0..1CodeableConceptWhy the result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

... note 0..*AnnotationComments about the observation
... bodySite 0..1CodeableConceptObserved body part
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.

... method 0..1CodeableConceptSequencing | Oligo aCGH | SNP array | BAC aCGH |Curated|+
Binding: LOINC Answer List LL4048-6 (extensible): Variant analysis method type

... specimen 0..1Reference(Specimen)Specimen examined
... device 0..1Reference(Device | DeviceMetric)(Measurement) Device
... referenceRange C0..*BackboneElementProvides guide for interpretation
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... low C0..1SimpleQuantityLow Range, if relevant
.... high C0..1SimpleQuantityHigh Range, if relevant
.... type 0..1CodeableConceptReference range qualifier
Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range.

.... appliesTo 0..*CodeableConceptReference range population
Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to.


.... age 0..1RangeApplicable age range, if relevant
.... text 0..1stringText based reference range in an observation
... hasMember Σ0..*Reference(Observation | QuestionnaireResponse | MolecularSequence)Related resource that belongs to the Observation group
... Slices for derivedFrom Σ1..*Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence)Related measurements the observation is made from
Slice: Unordered, Open by pattern:reference
.... derivedFrom:Analysis Σ1..1Reference(Sequencing Analysis)Analysis from which come this observation
... Slices for component Σ0..*BackboneElementComponent results
Slice: Unordered, Open by pattern:code
.... component:All Slices Content/Rules for all slices
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.

..... value[x] Σ0..1Actual component result
...... valueQuantityQuantity
...... valueCodeableConceptCodeableConcept
...... valueStringstring
...... valueBooleanboolean
...... valueIntegerinteger
...... valueRangeRange
...... valueRatioRatio
...... valueSampledDataSampledData
...... valueTimetime
...... valueDateTimedateTime
...... valuePeriodPeriod
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:gene-studied Σ0..*BackboneElementGene studied ID
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48018-6
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptIf no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HGNC (extensible): HGNC: Human Gene Nomenclature Committee

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:cytogenetic-location Σ0..*BackboneElementCytogenetic (chromosome) location
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48001-2
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptActual component result
Binding: (unbound) (example): Binding not yet defined

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:ref-sequence-assembly Σ0..*BackboneElementHuman reference sequence assembly version
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 62374-4
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptActual component result
Binding: LOINC Answer List LL1040-6 (extensible): Human reference sequence NCBI build IDs

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:dna-chg Σ0..1BackboneElementDNA Change - Transcript (cHGVS)
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48004-6
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptActual component result
Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:dna-chg-type Σ0..1BackboneElementDNA change type
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48019-4
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptConcepts in sequence ontology under SO:0002072 (see http://www.sequenceontology.org/browser/current_release/term/SO:0002072)
Binding: DNA Change Type (extensible): DNA Change type values (Sequence Ontology)

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:functional-annotation Σ0..*BackboneElementFunctional Annotation
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: functional-annotation
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptConcepts in sequence ontology under SO:0001537 (see http://www.sequenceontology.org/browser/current_release/term/SO:0001537)
Binding: Functional Annotation (extensible): Functional Annotation (Sequence Ontology)

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:variation-code Σ0..1BackboneElementVariation Code
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81252-9
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptActual component result
Binding: (unbound) (example): Binding not yet defined

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:dbSNP-id Σ0..1BackboneElementdbSNP ID
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81255-2
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptActual component result
Binding: (unbound) (example): Binding not yet defined

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:genomic-dna-chg Σ0..1BackboneElementDNA Change - Genomic (gHGVS)
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81290-9
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptActual component result
Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:genomic-source-class Σ0..1BackboneElementGenomic source class
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48002-0
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptGermline | Somatic | Fetal | Likely germline | Likely somatic |Likely fetal | Unknown genomic origin | De novo
Binding: LOINC Answer List LL378-1 (extensible): Genomic source class values

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:amino-acid-chg Σ0..1BackboneElementAmino acid change (pHGVS)
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48005-3
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptActual component result
Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:amino-acid-chg-type Σ0..1BackboneElementAmino acid change type
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48006-1
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptWild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Silent | Stop Codon Mutation
Binding: LOINC Answer List LL380-7 (required): Amino acid change type values

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:transcript-ref-seq Σ0..1BackboneElementTranscript reference sequence ID
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 51958-7
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptActual component result
Binding: (unbound) (example): Binding not yet defined

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:genomic-ref-seq Σ0..1BackboneElementGenomic reference sequence ID
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48013-7
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptActual component result
Binding: (unbound) (example): Binding not yet defined

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:sample-allelic-frequency Σ0..1BackboneElementSample Allelic Frequency
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptSample Sample VAF
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81258-6
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1QuantityActual component result
...... id 0..1stringUnique id for inter-element referencing
...... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
...... value Σ1..1decimalNumerical value (with implicit precision)
...... comparator ?!Σ0..1code< | <= | >= | > - how to understand the value
Binding: QuantityComparator (required): How the Quantity should be understood and represented.

...... unit Σ0..1stringUnit representation
...... system ΣC1..1uriSystem that defines coded unit form
Fixed Value: http://unitsofmeasure.org
...... code Σ0..1codeCoded form of the unit
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:allelic-read-depth Σ0..*BackboneElementAllelic read depth
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 82121-5
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1QuantityActual component result
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:allelic-state Σ0..1BackboneElementAllelic state
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 53034-5
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptHeteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (extensible): Allelic state type values

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:copy-number Σ0..1BackboneElementGenomic structural variant copy number
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 82155-3
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] C1..1CountA measured or measurable amount
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:ref-allele Σ0..1BackboneElementGenomic ref allele
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 69547-8
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1stringActual component result
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:alt-allele Σ0..1BackboneElementGenomic alt allele
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 69551-0
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1stringActual component result
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:coordinate-system Σ0..1BackboneElementCoordinate System
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 92822-6
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConcept0-based interval | 0-based character | 1-based character
Binding: LOINC Answer List LL5323-2 (preferred): Base coordinate systems start and end measurements for variants

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:exact-start-end Σ0..1BackboneElementExact start-end
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: exact-start-end
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1RangeActual component result
...... id 0..1stringUnique id for inter-element referencing
...... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
...... low Σ1..1SimpleQuantityExact Start
...... high Σ0..1SimpleQuantityExact End
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:variant-length Σ0..1BackboneElementStructural variant length
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81300-6
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] C1..1CountA measured or measurable amount
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:outer-start-end Σ0..1BackboneElementVariant outer start and end
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: outer-start-end
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1RangeActual component result
...... id 0..1stringUnique id for inter-element referencing
...... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
...... low Σ1..1SimpleQuantityLow limit
...... high Σ1..1SimpleQuantityHigh limit
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:inner-start-end Σ0..1BackboneElementVariant inner start and end
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: inner-start-end
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1RangeActual component result
...... id 0..1stringUnique id for inter-element referencing
...... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
...... low Σ1..1SimpleQuantityLow limit
...... high Σ1..1SimpleQuantityHigh limit
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:chromosome-copy-number-change-type Σ0..1BackboneElementChromosome copy number change type
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 62378-5
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptCopy number gain | Copy number loss
Binding: LOINC Answer List LL1041-4 (required): Copy Number Change Types

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:arrCGH-ratio Σ0..1BackboneElementStructural variant reported arrCGH [Ratio]
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81299-0
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] C1..1SimpleQuantityA fixed quantity (no comparator)
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:complex-var-type Σ0..1BackboneElementComplex variant type
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81263-6
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptCompound heterozygous | Double heterozygous | Haplotype | Hemizygous
Binding: LOINC Answer List LL3999-1 (required): Complex variant type

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:cytogenomic-nomenclature Σ0..1BackboneElementCytogenomic Nomenclature
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptVariant ISCN
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81291-7
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptActual component result
Binding: (unbound) (example): Binding not yet defined

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:variant-inheritance Σ0..1BackboneElementVariant Inheritance
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: variant-inheritance
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptActual component result
Binding: Variant Inheritance (extensible): Variant Inheritance (Sequence Ontology)

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:actionability Σ0..1BackboneElementConclusion of the clinicians wether the variant is actionable or not during the Molecular Tumor Board
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 93348-1
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... Slices for value[x] Σ0..1booleanActual component result
Slice: Unordered, Closed by type:$this
...... value[x]:valueBoolean Σ0..1booleanActual component result
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:proposed-for-orientation Σ0..1BackboneElementIs the ClinicalTumorBoardConclusion used to orient the treatment decision ?
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/umls
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: C0449889
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... Slices for value[x] Σ0..1booleanActual component result
Slice: Unordered, Closed by type:$this
...... value[x]:valueBoolean Σ0..1booleanActual component result
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:pathogenicity Σ0..1BackboneElementConclusion of the biologist on the pathogenicity of the variant before the Molecular Tumor Board
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 74019-1
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... Slices for value[x] Σ0..1CodeableConceptActual component result
Slice: Unordered, Closed by type:$this
Binding: Pathogenicity Value Set (required)
...... value[x]:valueCodeableConcept Σ0..1CodeableConceptActual component result
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:loss-of-heterozygosity Σ0..1BackboneElementIs the segment located in a region of loss of heterozygosity ? (can be independant from copy number information
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/umls
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: C1881449
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... Slices for value[x] Σ0..1booleanActual component result
Slice: Unordered, Closed by type:$this
...... value[x]:valueBoolean Σ0..1booleanActual component result
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:segment-intensity Σ0..1BackboneElementIntensity of the measured signal
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/umls
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: C2732930
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... Slices for value[x] Σ0..1integerActual component result
Slice: Unordered, Closed by type:$this
...... value[x]:valueInteger Σ0..1integerActual component result
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet / Code
Observation.languagepreferredCommonLanguages
Additional Bindings Purpose
AllLanguages Max Binding
Observation.statusrequiredObservationStatus
Observation.categorypreferredPattern: laboratory
Observation.codeexamplePattern: LOINC code 69548-6
Observation.value[x]requiredLOINC LL1971-2
Observation.dataAbsentReasonextensibleDataAbsentReason
Observation.bodySiteexampleSNOMEDCTBodyStructures
Observation.methodextensibleLOINC LL4048-6
Observation.referenceRange.typepreferredObservationReferenceRangeMeaningCodes
Observation.referenceRange.appliesToexampleObservationReferenceRangeAppliesToCodes
Observation.component.codeexampleLOINCCodes (a valid code from LOINC)
Observation.component.dataAbsentReasonextensibleDataAbsentReason
Observation.component:gene-studied.codeexamplePattern: LOINC code 48018-6
Observation.component:gene-studied.value[x]extensibleHGNC
Observation.component:gene-studied.dataAbsentReasonextensibleDataAbsentReason
Observation.component:cytogenetic-location.codeexamplePattern: LOINC code 48001-2
Observation.component:cytogenetic-location.value[x]example
Observation.component:cytogenetic-location.dataAbsentReasonextensibleDataAbsentReason
Observation.component:ref-sequence-assembly.codeexamplePattern: LOINC code 62374-4
Observation.component:ref-sequence-assembly.value[x]extensibleLOINC LL1040-6
Observation.component:ref-sequence-assembly.dataAbsentReasonextensibleDataAbsentReason
Observation.component:dna-chg.codeexamplePattern: LOINC code 48004-6
Observation.component:dna-chg.value[x]requiredHGVS
Observation.component:dna-chg.dataAbsentReasonextensibleDataAbsentReason
Observation.component:dna-chg-type.codeexamplePattern: LOINC code 48019-4
Observation.component:dna-chg-type.value[x]extensibleDnaChangeType
Observation.component:dna-chg-type.dataAbsentReasonextensibleDataAbsentReason
Observation.component:functional-annotation.codeexamplePattern: functional-annotation
Observation.component:functional-annotation.value[x]extensibleFunctionalAnnotation
Observation.component:functional-annotation.dataAbsentReasonextensibleDataAbsentReason
Observation.component:variation-code.codeexamplePattern: LOINC code 81252-9
Observation.component:variation-code.value[x]example
Observation.component:variation-code.dataAbsentReasonextensibleDataAbsentReason
Observation.component:dbSNP-id.codeexamplePattern: LOINC code 81255-2
Observation.component:dbSNP-id.value[x]example
Observation.component:dbSNP-id.dataAbsentReasonextensibleDataAbsentReason
Observation.component:genomic-dna-chg.codeexamplePattern: LOINC code 81290-9
Observation.component:genomic-dna-chg.value[x]requiredHGVS
Observation.component:genomic-dna-chg.dataAbsentReasonextensibleDataAbsentReason
Observation.component:genomic-source-class.codeexamplePattern: LOINC code 48002-0
Observation.component:genomic-source-class.value[x]extensibleLOINC LL378-1
Observation.component:genomic-source-class.dataAbsentReasonextensibleDataAbsentReason
Observation.component:amino-acid-chg.codeexamplePattern: LOINC code 48005-3
Observation.component:amino-acid-chg.value[x]requiredHGVS
Observation.component:amino-acid-chg.dataAbsentReasonextensibleDataAbsentReason
Observation.component:amino-acid-chg-type.codeexamplePattern: LOINC code 48006-1
Observation.component:amino-acid-chg-type.value[x]requiredLOINC LL380-7
Observation.component:amino-acid-chg-type.dataAbsentReasonextensibleDataAbsentReason
Observation.component:transcript-ref-seq.codeexamplePattern: LOINC code 51958-7
Observation.component:transcript-ref-seq.value[x]example
Observation.component:transcript-ref-seq.dataAbsentReasonextensibleDataAbsentReason
Observation.component:genomic-ref-seq.codeexamplePattern: LOINC code 48013-7
Observation.component:genomic-ref-seq.value[x]example
Observation.component:genomic-ref-seq.dataAbsentReasonextensibleDataAbsentReason
Observation.component:sample-allelic-frequency.codeexamplePattern: LOINC code 81258-6
Observation.component:sample-allelic-frequency.value[x].comparatorrequiredQuantityComparator
Observation.component:sample-allelic-frequency.dataAbsentReasonextensibleDataAbsentReason
Observation.component:allelic-read-depth.codeexamplePattern: LOINC code 82121-5
Observation.component:allelic-read-depth.dataAbsentReasonextensibleDataAbsentReason
Observation.component:allelic-state.codeexamplePattern: LOINC code 53034-5
Observation.component:allelic-state.value[x]extensibleLOINC LL381-5
Observation.component:allelic-state.dataAbsentReasonextensibleDataAbsentReason
Observation.component:copy-number.codeexamplePattern: LOINC code 82155-3
Observation.component:copy-number.dataAbsentReasonextensibleDataAbsentReason
Observation.component:ref-allele.codeexamplePattern: LOINC code 69547-8
Observation.component:ref-allele.dataAbsentReasonextensibleDataAbsentReason
Observation.component:alt-allele.codeexamplePattern: LOINC code 69551-0
Observation.component:alt-allele.dataAbsentReasonextensibleDataAbsentReason
Observation.component:coordinate-system.codeexamplePattern: LOINC code 92822-6
Observation.component:coordinate-system.value[x]preferredLOINC LL5323-2
Observation.component:coordinate-system.dataAbsentReasonextensibleDataAbsentReason
Observation.component:exact-start-end.codeexamplePattern: exact-start-end
Observation.component:exact-start-end.dataAbsentReasonextensibleDataAbsentReason
Observation.component:variant-length.codeexamplePattern: LOINC code 81300-6
Observation.component:variant-length.dataAbsentReasonextensibleDataAbsentReason
Observation.component:outer-start-end.codeexamplePattern: outer-start-end
Observation.component:outer-start-end.dataAbsentReasonextensibleDataAbsentReason
Observation.component:inner-start-end.codeexamplePattern: inner-start-end
Observation.component:inner-start-end.dataAbsentReasonextensibleDataAbsentReason
Observation.component:chromosome-copy-number-change-type.codeexamplePattern: LOINC code 62378-5
Observation.component:chromosome-copy-number-change-type.value[x]requiredLOINC LL1041-4
Observation.component:chromosome-copy-number-change-type.dataAbsentReasonextensibleDataAbsentReason
Observation.component:arrCGH-ratio.codeexamplePattern: LOINC code 81299-0
Observation.component:arrCGH-ratio.dataAbsentReasonextensibleDataAbsentReason
Observation.component:complex-var-type.codeexamplePattern: LOINC code 81263-6
Observation.component:complex-var-type.value[x]requiredLOINC LL3999-1
Observation.component:complex-var-type.dataAbsentReasonextensibleDataAbsentReason
Observation.component:cytogenomic-nomenclature.codeexamplePattern: LOINC code 81291-7
Observation.component:cytogenomic-nomenclature.value[x]example
Observation.component:cytogenomic-nomenclature.dataAbsentReasonextensibleDataAbsentReason
Observation.component:variant-inheritance.codeexamplePattern: variant-inheritance
Observation.component:variant-inheritance.value[x]extensibleVariantInheritance
Observation.component:variant-inheritance.dataAbsentReasonextensibleDataAbsentReason
Observation.component:actionability.codeexamplePattern: LOINC code 93348-1
Observation.component:actionability.dataAbsentReasonextensibleDataAbsentReason
Observation.component:proposed-for-orientation.codeexamplePattern: C0449889
Observation.component:proposed-for-orientation.dataAbsentReasonextensibleDataAbsentReason
Observation.component:pathogenicity.codeexamplePattern: LOINC code 74019-1
Observation.component:pathogenicity.value[x]requiredPathogenicity
Observation.component:pathogenicity.dataAbsentReasonextensibleDataAbsentReason
Observation.component:loss-of-heterozygosity.codeexamplePattern: C1881449
Observation.component:loss-of-heterozygosity.dataAbsentReasonextensibleDataAbsentReason
Observation.component:segment-intensity.codeexamplePattern: C2732930
Observation.component:segment-intensity.dataAbsentReasonextensibleDataAbsentReason

This structure is derived from Variant

Summary

Mandatory: 2 elements (4 nested mandatory elements)

Structures

This structure refers to these other structures:

Slices

This structure defines the following Slices:

  • The element Observation.derivedFrom is sliced based on the value of pattern:reference
  • The element Observation.component.value[x] is sliced based on the value of type:$this

Differential View

This structure is derived from Variant

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation 0..*VariantVariant
... subject 0..1Reference(Oncology Patient)Who and/or what the observation is about
... Slices for derivedFrom 1..*Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence)Related measurements the observation is made from
Slice: Unordered, Open by pattern:reference
.... derivedFrom:Analysis 1..1Reference(Sequencing Analysis)Analysis from which come this observation
.... component:cytogenetic-location 0..*BackboneElementCytogenetic (chromosome) location
.... component:ref-sequence-assembly 0..*BackboneElementHuman reference sequence assembly version
..... valueCodeableConcept 1..1CodeableConceptActual component result
.... component:variation-code 0..1BackboneElementVariation Code
..... valueCodeableConcept 1..1CodeableConceptActual component result
.... component:copy-number 0..1BackboneElementGenomic structural variant copy number
..... valueQuantity 1..1CountA measured or measurable amount
.... component:exact-start-end 0..1BackboneElementExact start-end
..... valueRange 1..1RangeActual component result
...... low 1..1SimpleQuantityExact Start
...... high 0..1SimpleQuantityExact End
.... component:variant-length 0..1BackboneElementStructural variant length
.... component:actionability 0..1BackboneElementConclusion of the clinicians wether the variant is actionable or not during the Molecular Tumor Board
..... code 1..1CodeableConceptType of component observation (code / type)
Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 93348-1
..... value[x] 0..1booleanActual component result
Slice: Unordered, Open by type:$this
..... valueBoolean 0..1booleanActual component result
.... component:proposed-for-orientation 0..1BackboneElementIs the ClinicalTumorBoardConclusion used to orient the treatment decision ?
..... code 1..1CodeableConceptType of component observation (code / type)
Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/umls
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: C0449889
..... value[x] 0..1booleanActual component result
Slice: Unordered, Open by type:$this
..... valueBoolean 0..1booleanActual component result
.... component:pathogenicity 0..1BackboneElementConclusion of the biologist on the pathogenicity of the variant before the Molecular Tumor Board
..... code 1..1CodeableConceptType of component observation (code / type)
Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 74019-1
..... value[x] 0..1CodeableConceptActual component result
Slice: Unordered, Open by type:$this
Binding: Pathogenicity Value Set (required)
..... valueCodeableConcept 0..1CodeableConceptActual component result
.... component:loss-of-heterozygosity 0..1BackboneElementIs the segment located in a region of loss of heterozygosity ? (can be independant from copy number information
..... code 1..1CodeableConceptType of component observation (code / type)
Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/umls
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: C1881449
..... value[x] 0..1booleanActual component result
Slice: Unordered, Open by type:$this
..... valueBoolean 0..1booleanActual component result
.... component:segment-intensity 0..1BackboneElementIntensity of the measured signal
..... code 1..1CodeableConceptType of component observation (code / type)
Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/umls
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: C2732930
..... value[x] 0..1integerActual component result
Slice: Unordered, Open by type:$this
..... valueInteger 0..1integerActual component result

doco Documentation for this format

Terminology Bindings (Differential)

PathConformanceValueSet
Observation.component:pathogenicity.value[x]requiredPathogenicity

Key Elements View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation C0..*VariantVariant
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... BodyStructure 0..1Reference(BodyStructure)Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
... SecondaryFinding 0..1CodeableConceptSecondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings
URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding
Binding: ObservationCategoryCodes (extensible): Codes to denote a guideline or policy statement.when a genetic test result is being shared as a secondary finding.


... status ?!Σ1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.

... category 1..*CodeableConceptClassification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.



Required Pattern: At least the following
.... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
..... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
... code Σ1..1CodeableConceptGenetic variant assessment
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
.... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
..... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: 69548-6
... subject Σ0..1Reference(Oncology Patient)Who and/or what the observation is about
... Slices for effective[x] Σ0..1dateTimeClinically relevant time/time-period for observation
Slice: Unordered, Closed by type:$this
.... effective[x]:effectiveDateTime Σ0..1dateTimeClinically relevant time/time-period for observation
... performer Σ0..1Reference(Practitioner | Organization | Patient | RelatedPerson)Who is responsible for the observation
... value[x] ΣC1..1CodeableConceptPresent|Absent|No call|Indeterminate
Binding: LOINC Answer List LL1971-2 (required): Genetic Variant Assessment

... Slices for derivedFrom Σ1..*Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence)Related measurements the observation is made from
Slice: Unordered, Open by pattern:reference
.... derivedFrom:Analysis Σ1..1Reference(Sequencing Analysis)Analysis from which come this observation
... Slices for component Σ0..*BackboneElementComponent results
Slice: Unordered, Open by pattern:code
.... component:All Slices Content/Rules for all slices
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.

.... component:gene-studied Σ0..*BackboneElementGene studied ID
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48018-6
..... value[x] Σ1..1CodeableConceptIf no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HGNC (extensible): HGNC: Human Gene Nomenclature Committee

.... component:cytogenetic-location Σ0..*BackboneElementCytogenetic (chromosome) location
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48001-2
..... value[x] Σ1..1CodeableConceptActual component result
Binding: (unbound) (example): Binding not yet defined

.... component:ref-sequence-assembly Σ0..*BackboneElementHuman reference sequence assembly version
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 62374-4
..... value[x] Σ1..1CodeableConceptActual component result
Binding: LOINC Answer List LL1040-6 (extensible): Human reference sequence NCBI build IDs

.... component:dna-chg Σ0..1BackboneElementDNA Change - Transcript (cHGVS)
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48004-6
..... value[x] Σ1..1CodeableConceptActual component result
Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society

.... component:dna-chg-type Σ0..1BackboneElementDNA change type
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48019-4
..... value[x] Σ1..1CodeableConceptConcepts in sequence ontology under SO:0002072 (see http://www.sequenceontology.org/browser/current_release/term/SO:0002072)
Binding: DNA Change Type (extensible): DNA Change type values (Sequence Ontology)

.... component:functional-annotation Σ0..*BackboneElementFunctional Annotation
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: functional-annotation
..... value[x] Σ1..1CodeableConceptConcepts in sequence ontology under SO:0001537 (see http://www.sequenceontology.org/browser/current_release/term/SO:0001537)
Binding: Functional Annotation (extensible): Functional Annotation (Sequence Ontology)

.... component:variation-code Σ0..1BackboneElementVariation Code
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81252-9
..... value[x] Σ1..1CodeableConceptActual component result
Binding: (unbound) (example): Binding not yet defined

.... component:dbSNP-id Σ0..1BackboneElementdbSNP ID
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81255-2
..... value[x] Σ1..1CodeableConceptActual component result
Binding: (unbound) (example): Binding not yet defined

.... component:genomic-dna-chg Σ0..1BackboneElementDNA Change - Genomic (gHGVS)
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81290-9
..... value[x] Σ1..1CodeableConceptActual component result
Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society

.... component:genomic-source-class Σ0..1BackboneElementGenomic source class
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48002-0
..... value[x] Σ1..1CodeableConceptGermline | Somatic | Fetal | Likely germline | Likely somatic |Likely fetal | Unknown genomic origin | De novo
Binding: LOINC Answer List LL378-1 (extensible): Genomic source class values

.... component:amino-acid-chg Σ0..1BackboneElementAmino acid change (pHGVS)
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48005-3
..... value[x] Σ1..1CodeableConceptActual component result
Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society

.... component:amino-acid-chg-type Σ0..1BackboneElementAmino acid change type
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48006-1
..... value[x] Σ1..1CodeableConceptWild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Silent | Stop Codon Mutation
Binding: LOINC Answer List LL380-7 (required): Amino acid change type values

.... component:transcript-ref-seq Σ0..1BackboneElementTranscript reference sequence ID
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 51958-7
..... value[x] Σ1..1CodeableConceptActual component result
Binding: (unbound) (example): Binding not yet defined

.... component:genomic-ref-seq Σ0..1BackboneElementGenomic reference sequence ID
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48013-7
..... value[x] Σ1..1CodeableConceptActual component result
Binding: (unbound) (example): Binding not yet defined

.... component:sample-allelic-frequency Σ0..1BackboneElementSample Allelic Frequency
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptSample Sample VAF
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81258-6
..... value[x] Σ1..1QuantityActual component result
...... value Σ1..1decimalNumerical value (with implicit precision)
...... comparator ?!Σ0..1code< | <= | >= | > - how to understand the value
Binding: QuantityComparator (required): How the Quantity should be understood and represented.

...... system ΣC1..1uriSystem that defines coded unit form
Fixed Value: http://unitsofmeasure.org
.... component:allelic-read-depth Σ0..*BackboneElementAllelic read depth
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 82121-5
..... value[x] Σ1..1QuantityActual component result
.... component:allelic-state Σ0..1BackboneElementAllelic state
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 53034-5
..... value[x] Σ1..1CodeableConceptHeteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (extensible): Allelic state type values

.... component:copy-number Σ0..1BackboneElementGenomic structural variant copy number
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 82155-3
..... value[x] C1..1CountA measured or measurable amount
.... component:ref-allele Σ0..1BackboneElementGenomic ref allele
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 69547-8
..... value[x] Σ1..1stringActual component result
.... component:alt-allele Σ0..1BackboneElementGenomic alt allele
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 69551-0
..... value[x] Σ1..1stringActual component result
.... component:coordinate-system Σ0..1BackboneElementCoordinate System
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 92822-6
..... value[x] Σ1..1CodeableConcept0-based interval | 0-based character | 1-based character
Binding: LOINC Answer List LL5323-2 (preferred): Base coordinate systems start and end measurements for variants

.... component:exact-start-end Σ0..1BackboneElementExact start-end
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: exact-start-end
..... value[x] Σ1..1RangeActual component result
...... low Σ1..1SimpleQuantityExact Start
.... component:variant-length Σ0..1BackboneElementStructural variant length
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81300-6
..... value[x] C1..1CountA measured or measurable amount
.... component:outer-start-end Σ0..1BackboneElementVariant outer start and end
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: outer-start-end
..... value[x] Σ1..1RangeActual component result
...... low Σ1..1SimpleQuantityLow limit
...... high Σ1..1SimpleQuantityHigh limit
.... component:inner-start-end Σ0..1BackboneElementVariant inner start and end
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: inner-start-end
..... value[x] Σ1..1RangeActual component result
...... low Σ1..1SimpleQuantityLow limit
...... high Σ1..1SimpleQuantityHigh limit
.... component:chromosome-copy-number-change-type Σ0..1BackboneElementChromosome copy number change type
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 62378-5
..... value[x] Σ1..1CodeableConceptCopy number gain | Copy number loss
Binding: LOINC Answer List LL1041-4 (required): Copy Number Change Types

.... component:arrCGH-ratio Σ0..1BackboneElementStructural variant reported arrCGH [Ratio]
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81299-0
..... value[x] C1..1SimpleQuantityA fixed quantity (no comparator)
.... component:complex-var-type Σ0..1BackboneElementComplex variant type
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81263-6
..... value[x] Σ1..1CodeableConceptCompound heterozygous | Double heterozygous | Haplotype | Hemizygous
Binding: LOINC Answer List LL3999-1 (required): Complex variant type

.... component:cytogenomic-nomenclature Σ0..1BackboneElementCytogenomic Nomenclature
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptVariant ISCN
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81291-7
..... value[x] Σ1..1CodeableConceptActual component result
Binding: (unbound) (example): Binding not yet defined

.... component:variant-inheritance Σ0..1BackboneElementVariant Inheritance
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: variant-inheritance
..... value[x] Σ1..1CodeableConceptActual component result
Binding: Variant Inheritance (extensible): Variant Inheritance (Sequence Ontology)

.... component:actionability Σ0..1BackboneElementConclusion of the clinicians wether the variant is actionable or not during the Molecular Tumor Board
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 93348-1
..... Slices for value[x] Σ0..1booleanActual component result
Slice: Unordered, Closed by type:$this
...... value[x]:valueBoolean Σ0..1booleanActual component result
.... component:proposed-for-orientation Σ0..1BackboneElementIs the ClinicalTumorBoardConclusion used to orient the treatment decision ?
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/umls
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: C0449889
..... Slices for value[x] Σ0..1booleanActual component result
Slice: Unordered, Closed by type:$this
...... value[x]:valueBoolean Σ0..1booleanActual component result
.... component:pathogenicity Σ0..1BackboneElementConclusion of the biologist on the pathogenicity of the variant before the Molecular Tumor Board
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 74019-1
..... Slices for value[x] Σ0..1CodeableConceptActual component result
Slice: Unordered, Closed by type:$this
Binding: Pathogenicity Value Set (required)
...... value[x]:valueCodeableConcept Σ0..1CodeableConceptActual component result
.... component:loss-of-heterozygosity Σ0..1BackboneElementIs the segment located in a region of loss of heterozygosity ? (can be independant from copy number information
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/umls
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: C1881449
..... Slices for value[x] Σ0..1booleanActual component result
Slice: Unordered, Closed by type:$this
...... value[x]:valueBoolean Σ0..1booleanActual component result
.... component:segment-intensity Σ0..1BackboneElementIntensity of the measured signal
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/umls
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: C2732930
..... Slices for value[x] Σ0..1integerActual component result
Slice: Unordered, Closed by type:$this
...... value[x]:valueInteger Σ0..1integerActual component result

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet / Code
Observation.statusrequiredObservationStatus
Observation.categorypreferredPattern: laboratory
Observation.codeexamplePattern: LOINC code 69548-6
Observation.value[x]requiredLOINC LL1971-2
Observation.component.codeexampleLOINCCodes (a valid code from LOINC)
Observation.component:gene-studied.codeexamplePattern: LOINC code 48018-6
Observation.component:gene-studied.value[x]extensibleHGNC
Observation.component:cytogenetic-location.codeexamplePattern: LOINC code 48001-2
Observation.component:cytogenetic-location.value[x]example
Observation.component:ref-sequence-assembly.codeexamplePattern: LOINC code 62374-4
Observation.component:ref-sequence-assembly.value[x]extensibleLOINC LL1040-6
Observation.component:dna-chg.codeexamplePattern: LOINC code 48004-6
Observation.component:dna-chg.value[x]requiredHGVS
Observation.component:dna-chg-type.codeexamplePattern: LOINC code 48019-4
Observation.component:dna-chg-type.value[x]extensibleDnaChangeType
Observation.component:functional-annotation.codeexamplePattern: functional-annotation
Observation.component:functional-annotation.value[x]extensibleFunctionalAnnotation
Observation.component:variation-code.codeexamplePattern: LOINC code 81252-9
Observation.component:variation-code.value[x]example
Observation.component:dbSNP-id.codeexamplePattern: LOINC code 81255-2
Observation.component:dbSNP-id.value[x]example
Observation.component:genomic-dna-chg.codeexamplePattern: LOINC code 81290-9
Observation.component:genomic-dna-chg.value[x]requiredHGVS
Observation.component:genomic-source-class.codeexamplePattern: LOINC code 48002-0
Observation.component:genomic-source-class.value[x]extensibleLOINC LL378-1
Observation.component:amino-acid-chg.codeexamplePattern: LOINC code 48005-3
Observation.component:amino-acid-chg.value[x]requiredHGVS
Observation.component:amino-acid-chg-type.codeexamplePattern: LOINC code 48006-1
Observation.component:amino-acid-chg-type.value[x]requiredLOINC LL380-7
Observation.component:transcript-ref-seq.codeexamplePattern: LOINC code 51958-7
Observation.component:transcript-ref-seq.value[x]example
Observation.component:genomic-ref-seq.codeexamplePattern: LOINC code 48013-7
Observation.component:genomic-ref-seq.value[x]example
Observation.component:sample-allelic-frequency.codeexamplePattern: LOINC code 81258-6
Observation.component:sample-allelic-frequency.value[x].comparatorrequiredQuantityComparator
Observation.component:allelic-read-depth.codeexamplePattern: LOINC code 82121-5
Observation.component:allelic-state.codeexamplePattern: LOINC code 53034-5
Observation.component:allelic-state.value[x]extensibleLOINC LL381-5
Observation.component:copy-number.codeexamplePattern: LOINC code 82155-3
Observation.component:ref-allele.codeexamplePattern: LOINC code 69547-8
Observation.component:alt-allele.codeexamplePattern: LOINC code 69551-0
Observation.component:coordinate-system.codeexamplePattern: LOINC code 92822-6
Observation.component:coordinate-system.value[x]preferredLOINC LL5323-2
Observation.component:exact-start-end.codeexamplePattern: exact-start-end
Observation.component:variant-length.codeexamplePattern: LOINC code 81300-6
Observation.component:outer-start-end.codeexamplePattern: outer-start-end
Observation.component:inner-start-end.codeexamplePattern: inner-start-end
Observation.component:chromosome-copy-number-change-type.codeexamplePattern: LOINC code 62378-5
Observation.component:chromosome-copy-number-change-type.value[x]requiredLOINC LL1041-4
Observation.component:arrCGH-ratio.codeexamplePattern: LOINC code 81299-0
Observation.component:complex-var-type.codeexamplePattern: LOINC code 81263-6
Observation.component:complex-var-type.value[x]requiredLOINC LL3999-1
Observation.component:cytogenomic-nomenclature.codeexamplePattern: LOINC code 81291-7
Observation.component:cytogenomic-nomenclature.value[x]example
Observation.component:variant-inheritance.codeexamplePattern: variant-inheritance
Observation.component:variant-inheritance.value[x]extensibleVariantInheritance
Observation.component:actionability.codeexamplePattern: LOINC code 93348-1
Observation.component:proposed-for-orientation.codeexamplePattern: C0449889
Observation.component:pathogenicity.codeexamplePattern: LOINC code 74019-1
Observation.component:pathogenicity.value[x]requiredPathogenicity
Observation.component:loss-of-heterozygosity.codeexamplePattern: C1881449
Observation.component:segment-intensity.codeexamplePattern: C2732930

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation C0..*VariantVariant
... id Σ0..1idLogical id of this artifact
... meta Σ0..1MetaMetadata about the resource
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: CommonLanguages (preferred): A human language.

Additional BindingsPurpose
AllLanguagesMax Binding
... text 0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... Slices for extension 0..*ExtensionExtension
Slice: Unordered, Open by value:url
... BodyStructure 0..1Reference(BodyStructure)Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
... SecondaryFinding 0..1CodeableConceptSecondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings
URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding
Binding: ObservationCategoryCodes (extensible): Codes to denote a guideline or policy statement.when a genetic test result is being shared as a secondary finding.


... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier Σ0..*IdentifierBusiness Identifier for observation
... basedOn Σ0..*Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)Fulfills plan, proposal or order
... partOf Σ0..*Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy)Part of referenced event
... status ?!Σ1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.

... category 1..*CodeableConceptClassification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.



Required Pattern: At least the following
.... id0..1idUnique id for inter-element referencing
.... extension0..*ExtensionAdditional content defined by implementations
.... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
..... id0..1idUnique id for inter-element referencing
..... extension0..*ExtensionAdditional content defined by implementations
..... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
..... version0..1stringVersion of the system - if relevant
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
..... display0..1stringRepresentation defined by the system
..... userSelected0..1booleanIf this coding was chosen directly by the user
.... text0..1stringPlain text representation of the concept
... code Σ1..1CodeableConceptGenetic variant assessment
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
.... id0..1idUnique id for inter-element referencing
.... extension0..*ExtensionAdditional content defined by implementations
.... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
..... id0..1idUnique id for inter-element referencing
..... extension0..*ExtensionAdditional content defined by implementations
..... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
..... version0..1stringVersion of the system - if relevant
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: 69548-6
..... display0..1stringRepresentation defined by the system
..... userSelected0..1booleanIf this coding was chosen directly by the user
.... text0..1stringPlain text representation of the concept
... subject Σ0..1Reference(Oncology Patient)Who and/or what the observation is about
... focus ΣTU0..*Reference(Resource)What the observation is about, when it is not about the subject of record
... encounter Σ0..1Reference(Encounter)Healthcare event during which this observation is made
... Slices for effective[x] Σ0..1dateTimeClinically relevant time/time-period for observation
Slice: Unordered, Closed by type:$this
.... effective[x]:effectiveDateTime Σ0..1dateTimeClinically relevant time/time-period for observation
... issued Σ0..1instantDate/Time this version was made available
... performer Σ0..1Reference(Practitioner | Organization | Patient | RelatedPerson)Who is responsible for the observation
... value[x] ΣC1..1CodeableConceptPresent|Absent|No call|Indeterminate
Binding: LOINC Answer List LL1971-2 (required): Genetic Variant Assessment

... dataAbsentReason C0..1CodeableConceptWhy the result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

... note 0..*AnnotationComments about the observation
... bodySite 0..1CodeableConceptObserved body part
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.

... method 0..1CodeableConceptSequencing | Oligo aCGH | SNP array | BAC aCGH |Curated|+
Binding: LOINC Answer List LL4048-6 (extensible): Variant analysis method type

... specimen 0..1Reference(Specimen)Specimen examined
... device 0..1Reference(Device | DeviceMetric)(Measurement) Device
... referenceRange C0..*BackboneElementProvides guide for interpretation
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... low C0..1SimpleQuantityLow Range, if relevant
.... high C0..1SimpleQuantityHigh Range, if relevant
.... type 0..1CodeableConceptReference range qualifier
Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range.

.... appliesTo 0..*CodeableConceptReference range population
Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to.


.... age 0..1RangeApplicable age range, if relevant
.... text 0..1stringText based reference range in an observation
... hasMember Σ0..*Reference(Observation | QuestionnaireResponse | MolecularSequence)Related resource that belongs to the Observation group
... Slices for derivedFrom Σ1..*Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence)Related measurements the observation is made from
Slice: Unordered, Open by pattern:reference
.... derivedFrom:Analysis Σ1..1Reference(Sequencing Analysis)Analysis from which come this observation
... Slices for component Σ0..*BackboneElementComponent results
Slice: Unordered, Open by pattern:code
.... component:All Slices Content/Rules for all slices
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.

..... value[x] Σ0..1Actual component result
...... valueQuantityQuantity
...... valueCodeableConceptCodeableConcept
...... valueStringstring
...... valueBooleanboolean
...... valueIntegerinteger
...... valueRangeRange
...... valueRatioRatio
...... valueSampledDataSampledData
...... valueTimetime
...... valueDateTimedateTime
...... valuePeriodPeriod
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:gene-studied Σ0..*BackboneElementGene studied ID
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48018-6
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptIf no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HGNC (extensible): HGNC: Human Gene Nomenclature Committee

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:cytogenetic-location Σ0..*BackboneElementCytogenetic (chromosome) location
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48001-2
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptActual component result
Binding: (unbound) (example): Binding not yet defined

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:ref-sequence-assembly Σ0..*BackboneElementHuman reference sequence assembly version
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 62374-4
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptActual component result
Binding: LOINC Answer List LL1040-6 (extensible): Human reference sequence NCBI build IDs

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:dna-chg Σ0..1BackboneElementDNA Change - Transcript (cHGVS)
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48004-6
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptActual component result
Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:dna-chg-type Σ0..1BackboneElementDNA change type
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48019-4
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptConcepts in sequence ontology under SO:0002072 (see http://www.sequenceontology.org/browser/current_release/term/SO:0002072)
Binding: DNA Change Type (extensible): DNA Change type values (Sequence Ontology)

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:functional-annotation Σ0..*BackboneElementFunctional Annotation
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: functional-annotation
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptConcepts in sequence ontology under SO:0001537 (see http://www.sequenceontology.org/browser/current_release/term/SO:0001537)
Binding: Functional Annotation (extensible): Functional Annotation (Sequence Ontology)

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:variation-code Σ0..1BackboneElementVariation Code
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81252-9
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptActual component result
Binding: (unbound) (example): Binding not yet defined

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:dbSNP-id Σ0..1BackboneElementdbSNP ID
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81255-2
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptActual component result
Binding: (unbound) (example): Binding not yet defined

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:genomic-dna-chg Σ0..1BackboneElementDNA Change - Genomic (gHGVS)
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81290-9
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptActual component result
Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:genomic-source-class Σ0..1BackboneElementGenomic source class
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48002-0
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptGermline | Somatic | Fetal | Likely germline | Likely somatic |Likely fetal | Unknown genomic origin | De novo
Binding: LOINC Answer List LL378-1 (extensible): Genomic source class values

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:amino-acid-chg Σ0..1BackboneElementAmino acid change (pHGVS)
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48005-3
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptActual component result
Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:amino-acid-chg-type Σ0..1BackboneElementAmino acid change type
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48006-1
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptWild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Silent | Stop Codon Mutation
Binding: LOINC Answer List LL380-7 (required): Amino acid change type values

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:transcript-ref-seq Σ0..1BackboneElementTranscript reference sequence ID
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 51958-7
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptActual component result
Binding: (unbound) (example): Binding not yet defined

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:genomic-ref-seq Σ0..1BackboneElementGenomic reference sequence ID
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48013-7
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptActual component result
Binding: (unbound) (example): Binding not yet defined

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:sample-allelic-frequency Σ0..1BackboneElementSample Allelic Frequency
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptSample Sample VAF
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81258-6
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1QuantityActual component result
...... id 0..1stringUnique id for inter-element referencing
...... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
...... value Σ1..1decimalNumerical value (with implicit precision)
...... comparator ?!Σ0..1code< | <= | >= | > - how to understand the value
Binding: QuantityComparator (required): How the Quantity should be understood and represented.

...... unit Σ0..1stringUnit representation
...... system ΣC1..1uriSystem that defines coded unit form
Fixed Value: http://unitsofmeasure.org
...... code Σ0..1codeCoded form of the unit
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:allelic-read-depth Σ0..*BackboneElementAllelic read depth
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 82121-5
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1QuantityActual component result
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:allelic-state Σ0..1BackboneElementAllelic state
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 53034-5
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptHeteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (extensible): Allelic state type values

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:copy-number Σ0..1BackboneElementGenomic structural variant copy number
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 82155-3
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] C1..1CountA measured or measurable amount
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:ref-allele Σ0..1BackboneElementGenomic ref allele
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 69547-8
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1stringActual component result
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:alt-allele Σ0..1BackboneElementGenomic alt allele
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 69551-0
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1stringActual component result
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:coordinate-system Σ0..1BackboneElementCoordinate System
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 92822-6
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConcept0-based interval | 0-based character | 1-based character
Binding: LOINC Answer List LL5323-2 (preferred): Base coordinate systems start and end measurements for variants

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:exact-start-end Σ0..1BackboneElementExact start-end
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: exact-start-end
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1RangeActual component result
...... id 0..1stringUnique id for inter-element referencing
...... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
...... low Σ1..1SimpleQuantityExact Start
...... high Σ0..1SimpleQuantityExact End
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:variant-length Σ0..1BackboneElementStructural variant length
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81300-6
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] C1..1CountA measured or measurable amount
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:outer-start-end Σ0..1BackboneElementVariant outer start and end
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: outer-start-end
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1RangeActual component result
...... id 0..1stringUnique id for inter-element referencing
...... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
...... low Σ1..1SimpleQuantityLow limit
...... high Σ1..1SimpleQuantityHigh limit
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:inner-start-end Σ0..1BackboneElementVariant inner start and end
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: inner-start-end
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1RangeActual component result
...... id 0..1stringUnique id for inter-element referencing
...... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
...... low Σ1..1SimpleQuantityLow limit
...... high Σ1..1SimpleQuantityHigh limit
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:chromosome-copy-number-change-type Σ0..1BackboneElementChromosome copy number change type
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 62378-5
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptCopy number gain | Copy number loss
Binding: LOINC Answer List LL1041-4 (required): Copy Number Change Types

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:arrCGH-ratio Σ0..1BackboneElementStructural variant reported arrCGH [Ratio]
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81299-0
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] C1..1SimpleQuantityA fixed quantity (no comparator)
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:complex-var-type Σ0..1BackboneElementComplex variant type
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81263-6
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptCompound heterozygous | Double heterozygous | Haplotype | Hemizygous
Binding: LOINC Answer List LL3999-1 (required): Complex variant type

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:cytogenomic-nomenclature Σ0..1BackboneElementCytogenomic Nomenclature
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptVariant ISCN
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81291-7
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptActual component result
Binding: (unbound) (example): Binding not yet defined

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:variant-inheritance Σ0..1BackboneElementVariant Inheritance
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: variant-inheritance
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptActual component result
Binding: Variant Inheritance (extensible): Variant Inheritance (Sequence Ontology)

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:actionability Σ0..1BackboneElementConclusion of the clinicians wether the variant is actionable or not during the Molecular Tumor Board
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 93348-1
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... Slices for value[x] Σ0..1booleanActual component result
Slice: Unordered, Closed by type:$this
...... value[x]:valueBoolean Σ0..1booleanActual component result
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:proposed-for-orientation Σ0..1BackboneElementIs the ClinicalTumorBoardConclusion used to orient the treatment decision ?
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/umls
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: C0449889
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... Slices for value[x] Σ0..1booleanActual component result
Slice: Unordered, Closed by type:$this
...... value[x]:valueBoolean Σ0..1booleanActual component result
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:pathogenicity Σ0..1BackboneElementConclusion of the biologist on the pathogenicity of the variant before the Molecular Tumor Board
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 74019-1
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... Slices for value[x] Σ0..1CodeableConceptActual component result
Slice: Unordered, Closed by type:$this
Binding: Pathogenicity Value Set (required)
...... value[x]:valueCodeableConcept Σ0..1CodeableConceptActual component result
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:loss-of-heterozygosity Σ0..1BackboneElementIs the segment located in a region of loss of heterozygosity ? (can be independant from copy number information
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/umls
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: C1881449
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... Slices for value[x] Σ0..1booleanActual component result
Slice: Unordered, Closed by type:$this
...... value[x]:valueBoolean Σ0..1booleanActual component result
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:segment-intensity Σ0..1BackboneElementIntensity of the measured signal
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1idUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1idUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/umls
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: C2732930
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... Slices for value[x] Σ0..1integerActual component result
Slice: Unordered, Closed by type:$this
...... value[x]:valueInteger Σ0..1integerActual component result
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet / Code
Observation.languagepreferredCommonLanguages
Additional Bindings Purpose
AllLanguages Max Binding
Observation.statusrequiredObservationStatus
Observation.categorypreferredPattern: laboratory
Observation.codeexamplePattern: LOINC code 69548-6
Observation.value[x]requiredLOINC LL1971-2
Observation.dataAbsentReasonextensibleDataAbsentReason
Observation.bodySiteexampleSNOMEDCTBodyStructures
Observation.methodextensibleLOINC LL4048-6
Observation.referenceRange.typepreferredObservationReferenceRangeMeaningCodes
Observation.referenceRange.appliesToexampleObservationReferenceRangeAppliesToCodes
Observation.component.codeexampleLOINCCodes (a valid code from LOINC)
Observation.component.dataAbsentReasonextensibleDataAbsentReason
Observation.component:gene-studied.codeexamplePattern: LOINC code 48018-6
Observation.component:gene-studied.value[x]extensibleHGNC
Observation.component:gene-studied.dataAbsentReasonextensibleDataAbsentReason
Observation.component:cytogenetic-location.codeexamplePattern: LOINC code 48001-2
Observation.component:cytogenetic-location.value[x]example
Observation.component:cytogenetic-location.dataAbsentReasonextensibleDataAbsentReason
Observation.component:ref-sequence-assembly.codeexamplePattern: LOINC code 62374-4
Observation.component:ref-sequence-assembly.value[x]extensibleLOINC LL1040-6
Observation.component:ref-sequence-assembly.dataAbsentReasonextensibleDataAbsentReason
Observation.component:dna-chg.codeexamplePattern: LOINC code 48004-6
Observation.component:dna-chg.value[x]requiredHGVS
Observation.component:dna-chg.dataAbsentReasonextensibleDataAbsentReason
Observation.component:dna-chg-type.codeexamplePattern: LOINC code 48019-4
Observation.component:dna-chg-type.value[x]extensibleDnaChangeType
Observation.component:dna-chg-type.dataAbsentReasonextensibleDataAbsentReason
Observation.component:functional-annotation.codeexamplePattern: functional-annotation
Observation.component:functional-annotation.value[x]extensibleFunctionalAnnotation
Observation.component:functional-annotation.dataAbsentReasonextensibleDataAbsentReason
Observation.component:variation-code.codeexamplePattern: LOINC code 81252-9
Observation.component:variation-code.value[x]example
Observation.component:variation-code.dataAbsentReasonextensibleDataAbsentReason
Observation.component:dbSNP-id.codeexamplePattern: LOINC code 81255-2
Observation.component:dbSNP-id.value[x]example
Observation.component:dbSNP-id.dataAbsentReasonextensibleDataAbsentReason
Observation.component:genomic-dna-chg.codeexamplePattern: LOINC code 81290-9
Observation.component:genomic-dna-chg.value[x]requiredHGVS
Observation.component:genomic-dna-chg.dataAbsentReasonextensibleDataAbsentReason
Observation.component:genomic-source-class.codeexamplePattern: LOINC code 48002-0
Observation.component:genomic-source-class.value[x]extensibleLOINC LL378-1
Observation.component:genomic-source-class.dataAbsentReasonextensibleDataAbsentReason
Observation.component:amino-acid-chg.codeexamplePattern: LOINC code 48005-3
Observation.component:amino-acid-chg.value[x]requiredHGVS
Observation.component:amino-acid-chg.dataAbsentReasonextensibleDataAbsentReason
Observation.component:amino-acid-chg-type.codeexamplePattern: LOINC code 48006-1
Observation.component:amino-acid-chg-type.value[x]requiredLOINC LL380-7
Observation.component:amino-acid-chg-type.dataAbsentReasonextensibleDataAbsentReason
Observation.component:transcript-ref-seq.codeexamplePattern: LOINC code 51958-7
Observation.component:transcript-ref-seq.value[x]example
Observation.component:transcript-ref-seq.dataAbsentReasonextensibleDataAbsentReason
Observation.component:genomic-ref-seq.codeexamplePattern: LOINC code 48013-7
Observation.component:genomic-ref-seq.value[x]example
Observation.component:genomic-ref-seq.dataAbsentReasonextensibleDataAbsentReason
Observation.component:sample-allelic-frequency.codeexamplePattern: LOINC code 81258-6
Observation.component:sample-allelic-frequency.value[x].comparatorrequiredQuantityComparator
Observation.component:sample-allelic-frequency.dataAbsentReasonextensibleDataAbsentReason
Observation.component:allelic-read-depth.codeexamplePattern: LOINC code 82121-5
Observation.component:allelic-read-depth.dataAbsentReasonextensibleDataAbsentReason
Observation.component:allelic-state.codeexamplePattern: LOINC code 53034-5
Observation.component:allelic-state.value[x]extensibleLOINC LL381-5
Observation.component:allelic-state.dataAbsentReasonextensibleDataAbsentReason
Observation.component:copy-number.codeexamplePattern: LOINC code 82155-3
Observation.component:copy-number.dataAbsentReasonextensibleDataAbsentReason
Observation.component:ref-allele.codeexamplePattern: LOINC code 69547-8
Observation.component:ref-allele.dataAbsentReasonextensibleDataAbsentReason
Observation.component:alt-allele.codeexamplePattern: LOINC code 69551-0
Observation.component:alt-allele.dataAbsentReasonextensibleDataAbsentReason
Observation.component:coordinate-system.codeexamplePattern: LOINC code 92822-6
Observation.component:coordinate-system.value[x]preferredLOINC LL5323-2
Observation.component:coordinate-system.dataAbsentReasonextensibleDataAbsentReason
Observation.component:exact-start-end.codeexamplePattern: exact-start-end
Observation.component:exact-start-end.dataAbsentReasonextensibleDataAbsentReason
Observation.component:variant-length.codeexamplePattern: LOINC code 81300-6
Observation.component:variant-length.dataAbsentReasonextensibleDataAbsentReason
Observation.component:outer-start-end.codeexamplePattern: outer-start-end
Observation.component:outer-start-end.dataAbsentReasonextensibleDataAbsentReason
Observation.component:inner-start-end.codeexamplePattern: inner-start-end
Observation.component:inner-start-end.dataAbsentReasonextensibleDataAbsentReason
Observation.component:chromosome-copy-number-change-type.codeexamplePattern: LOINC code 62378-5
Observation.component:chromosome-copy-number-change-type.value[x]requiredLOINC LL1041-4
Observation.component:chromosome-copy-number-change-type.dataAbsentReasonextensibleDataAbsentReason
Observation.component:arrCGH-ratio.codeexamplePattern: LOINC code 81299-0
Observation.component:arrCGH-ratio.dataAbsentReasonextensibleDataAbsentReason
Observation.component:complex-var-type.codeexamplePattern: LOINC code 81263-6
Observation.component:complex-var-type.value[x]requiredLOINC LL3999-1
Observation.component:complex-var-type.dataAbsentReasonextensibleDataAbsentReason
Observation.component:cytogenomic-nomenclature.codeexamplePattern: LOINC code 81291-7
Observation.component:cytogenomic-nomenclature.value[x]example
Observation.component:cytogenomic-nomenclature.dataAbsentReasonextensibleDataAbsentReason
Observation.component:variant-inheritance.codeexamplePattern: variant-inheritance
Observation.component:variant-inheritance.value[x]extensibleVariantInheritance
Observation.component:variant-inheritance.dataAbsentReasonextensibleDataAbsentReason
Observation.component:actionability.codeexamplePattern: LOINC code 93348-1
Observation.component:actionability.dataAbsentReasonextensibleDataAbsentReason
Observation.component:proposed-for-orientation.codeexamplePattern: C0449889
Observation.component:proposed-for-orientation.dataAbsentReasonextensibleDataAbsentReason
Observation.component:pathogenicity.codeexamplePattern: LOINC code 74019-1
Observation.component:pathogenicity.value[x]requiredPathogenicity
Observation.component:pathogenicity.dataAbsentReasonextensibleDataAbsentReason
Observation.component:loss-of-heterozygosity.codeexamplePattern: C1881449
Observation.component:loss-of-heterozygosity.dataAbsentReasonextensibleDataAbsentReason
Observation.component:segment-intensity.codeexamplePattern: C2732930
Observation.component:segment-intensity.dataAbsentReasonextensibleDataAbsentReason

This structure is derived from Variant

Summary

Mandatory: 2 elements (4 nested mandatory elements)

Structures

This structure refers to these other structures:

Slices

This structure defines the following Slices:

  • The element Observation.derivedFrom is sliced based on the value of pattern:reference
  • The element Observation.component.value[x] is sliced based on the value of type:$this

 

Other representations of profile: CSV, Excel, Schematron